So, the question is how does Hyperlink Pro define an “incomplete” URL.
It’s a bit simplistic. Any valid path (i.e., the bit after the http:// or https://) that is not preceded by a forward slash / is considered incomplete.
So, for example, both http://www.p65warnings.ca.gov and p65warnings.ca.gov are considered incomplete.
Since you’re adding “https://www.” you get the double www bit.
As a workaround, before running Hyperlink Pro, search for all “www” and change it “/www”. That should ensure that those URLs are left alone by the script.
Afterwards, remove the / before the www. (Of course, taking care that you don’t turn http://www into http:/www).